sorry LK5.off is attached now!
On Thu, Apr 14, 2011 at 11:37 AM, Hashem Taha <htahaphd.gmail.com> wrote:
> I have attached the test.pdb file as well as the frcmod and lib files for
> 4S2 and LK5.
>
>
>
> On Thu, Apr 14, 2011 at 11:20 AM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> Your errors look weird; I haven't seen any like that before that I can
>> recall. Can you attach the PDBs you tried using?
>>
>> On Thu, Apr 14, 2011 at 8:11 AM, Hashem Taha <htahaphd.gmail.com> wrote:
>>
>> > Any suggestions???
>> >
>> > On Tue, Apr 12, 2011 at 8:56 PM, Hashem Taha <htahaphd.gmail.com>
>> wrote:
>> >
>> > > I have tried HOH, WAT and TP3 for the residue name for the crystal
>> water,
>> > > but no luck. The odd thing that I am confused about is that when the
>> > crystal
>> > > water is present without the probe attached to cysteine residue (i.e
>> the
>> > > native protein), the solvation occurs with no problem, and when the
>> probe
>> > is
>> > > attached and the crystal water is removed, it also works. So, I'm
>> really
>> > not
>> > > sure what the problem is. I've attached the leap.log file
>> > >
>> > >
>> > >
>> > > On Tue, Apr 12, 2011 at 9:20 AM, Daniel Roe <daniel.r.roe.gmail.com
>> > >wrote:
>> > >
>> > >> What is the residue name of the water in the PDB? I think it needs to
>> > >> be 'WAT' for leap to recognize it as a water. Attaching your full
>> leap
>> > >> output may help to debug your problem further.
>> > >>
>> > >> -Dan
>> > >>
>> > >> On Mon, Apr 11, 2011 at 4:09 PM, Hashem Taha <htahaphd.gmail.com>
>> > wrote:
>> > >> > Hi,
>> > >> >
>> > >> > I am trying to solvate a protein that has a probe attached to a
>> > cysteine
>> > >> > residue and includes one crystal water molecule. The leap input
>> file I
>> > >> am
>> > >> > using is included below. Basically, when I try to solvate the
>> system
>> > >> with
>> > >> > the crystal water included in the initial pdb, I get the message
>> > >> > "ContainerCenterAt(): Skipping atom w/ unknown position: O:O" and
>> the
>> > >> system
>> > >> > does not solvate properly (the number of water residues that leap
>> adds
>> > >> > is 169969). If I try removing the crystal water, solvateOct works
>> > fine,
>> > >> and
>> > >> > solvateOct also works without problems on the protein without the
>> > probe
>> > >> on
>> > >> > the cysteine residue. Please advise!
>> > >> >
>> > >> > source /usr/local/amber/amber10/dat/leap/cmd/leaprc.gaff
>> > >> > source /usr/local/amber/amber10/dat/leap/cmd/leaprc.ff03
>> > >> > loadamberparams /nfs/01/osu6030/libs/CY3.frcmod
>> > >> > loadOff /nfs/01/osu6030/libs/CY3.lib
>> > >> > loadamberparams /nfs/01/osu6030/libs/linkers/LK5.frcmod
>> > >> > loadOff /nfs/01/osu6030/libs/linkers/LK5.lib
>> > >> > loadamberparams /nfs/01/osu6030/libs/TAMs/4S2.frcmod
>> > >> > loadOff /nfs/01/osu6030/libs/TAMs/4S2.lib
>> > >> > loadamberparams /nfs/01/osu6030/libs/linkers/linktoCYS.frcmod
>> > >> >
>> > >> > p = loadpdb test.pdb
>> > >> > check p
>> > >> > set p head p.63.SG
>> > >> >
>> > >> > b = sequence {4S2 LK5 p}
>> > >> > check b
>> > >> >
>> > >> > addions b Cl- 0
>> > >> > solvateOct b TIP3PBOX 8
>> > >> > savepdb b test.pdb
>> > >> > saveamberparm b test.prmtop test.inpcrd
>> > >> >
>> > >> > quit
>> > >> > _______________________________________________
>> > >> > AMBER mailing list
>> > >> > AMBER.ambermd.org
>> > >> > http://lists.ambermd.org/mailman/listinfo/amber
>> > >> >
>> > >>
>> > >> _______________________________________________
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>> > >>
>> > >
>> > >
>> > _______________________________________________
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>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
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>>
>
>
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- application/octet-stream attachment: LK5.off
Received on Thu Apr 14 2011 - 09:00:04 PDT
